Aim: The aim of this review was to discuss the proteomics of exercise. Results: The sophisticated protein biochemical and mass spectrometric technologies can now be used to study subtle changes in protein concentration, isoform expression patterns, protein-protein interactions and/or post-translational modifications following physical exercise. Conclusion: Rapid advancements in molecular techniques and the streamlining of mass spectrometry-based proteomic workflows have enabled the establishment of global alterations in the concentration, isoform expression patterns, molecular interactions and posttranslational modifications of muscle proteins following physical exercise. Recent genetic advances in the field of molecular exercise science will heavily influence the design of future proteomic studies in sports science and sports medicine.